FANCD2 binding identifies conserved fragile sites at large transcribed genes in avian cells
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FANCD2 binding identifies conserved fragile sites at large transcribed genes in avian cells. / Pentzold, Constanze; Shah, Shiraz Ali; Hansen, Niels Richard; Le Tallec, Benoit; Seguin-Orlando, Andaine; Debatisse, Michelle; Lisby, Michael; Oestergaard, Vibe Hallundbæk.
In: Nucleic Acids Research, Vol. 46, No. 3, 2018, p. 1280-1294.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - FANCD2 binding identifies conserved fragile sites at large transcribed genes in avian cells
AU - Pentzold, Constanze
AU - Shah, Shiraz Ali
AU - Hansen, Niels Richard
AU - Le Tallec, Benoit
AU - Seguin-Orlando, Andaine
AU - Debatisse, Michelle
AU - Lisby, Michael
AU - Oestergaard, Vibe Hallundbæk
PY - 2018
Y1 - 2018
N2 - Common Chromosomal Fragile Sites (CFSs) are specific genomic regions prone to form breaks on metaphase chromosomes in response to replication stress. Moreover, CFSs are mutational hotspots in cancer genomes, showing that the mutational mechanisms that operate at CFSs are highly active in cancer cells. Orthologs of human CFSs are found in a number of other mammals, but the extent of CFS conservation beyond the mammalian lineage is unclear. Characterization of CFSs from distantly related organisms can provide new insight into the biology underlying CFSs. Here, we have mapped CFSs in an avian cell line. We find that, overall the most significant CFSs coincide with extremely large conserved genes, from which very long transcripts are produced. However, no significant correlation between any sequence characteristics and CFSs is found. Moreover, we identified putative early replicating fragile sites (ERFSs), which is a distinct class of fragile sites and we developed a fluctuation analysis revealing high mutation rates at the CFS gene PARK2, with deletions as the most prevalent mutation. Finally, we show that avian homologs of the human CFS genes despite their fragility have resisted the general intron size reduction observed in birds suggesting that CFSs have a conserved biological function.
AB - Common Chromosomal Fragile Sites (CFSs) are specific genomic regions prone to form breaks on metaphase chromosomes in response to replication stress. Moreover, CFSs are mutational hotspots in cancer genomes, showing that the mutational mechanisms that operate at CFSs are highly active in cancer cells. Orthologs of human CFSs are found in a number of other mammals, but the extent of CFS conservation beyond the mammalian lineage is unclear. Characterization of CFSs from distantly related organisms can provide new insight into the biology underlying CFSs. Here, we have mapped CFSs in an avian cell line. We find that, overall the most significant CFSs coincide with extremely large conserved genes, from which very long transcripts are produced. However, no significant correlation between any sequence characteristics and CFSs is found. Moreover, we identified putative early replicating fragile sites (ERFSs), which is a distinct class of fragile sites and we developed a fluctuation analysis revealing high mutation rates at the CFS gene PARK2, with deletions as the most prevalent mutation. Finally, we show that avian homologs of the human CFS genes despite their fragility have resisted the general intron size reduction observed in birds suggesting that CFSs have a conserved biological function.
U2 - 10.1093/nar/gkx1260
DO - 10.1093/nar/gkx1260
M3 - Journal article
C2 - 29253234
VL - 46
SP - 1280
EP - 1294
JO - Nucleic Acids Research
JF - Nucleic Acids Research
SN - 0305-1048
IS - 3
ER -
ID: 192786172